Pontanus was the son of Margaretha van Delen and Isaac Pietersz, the Dutch consul to Denmark stationed in Helsingør. The painter Pieter Isaacsz (1568–1625) was his older brother. In 1578 his family returned to the Netherlands and Pontanus grew up in Amsterdam. In 1589 he enrolled as a medical student at the University of Franeker and in 1592 at Leiden University as "Joannes Hellespontius Danus", predating the apparent contraction "Pontanus" (he was said to be born at sea near Helsingør in the Danish Hellespont, the Øresund). The next year he defended his Dissertatio de rationalis animas facilitate and traveled to Rome, visiting German scholars on his return trip. Subsequently, Pontanus visited Denmark where his parents had returned and became acquainted with Tycho Brahe and Arild Huitfeldt. 1596 he spent mostly in England, visiting Canterbury, Oxford and Stanford. The following years he traveled to German, Swiss and French cities, in part escorting three young family members of Brahe.
In 1604 he was appointed professor at the Gelderse Academie in Harderwijk, where he remained teaching the rest of his life. He is best known for writing histories of places and countries. His history of Amsterdam (1611) was considered the first of this city. It was controversial enough to be blacklisted by the Roman church. In 1618 he was asked to write a history of Denmark, for which he was appointed as the Royal Danish official historian; he continued writing this work until his death but only managed to publish the first part in 1631. In 1621 he was asked to write a history of Guelders which he based largely on work of Paullus Merula en Johannes Luntius and finished in 1639.
Pontanus married Anneken van den Herde (or Heerde, Heede) in June 1606. They had at least four children. He died in Harderwijk in 1639, nine years before the academy was officially declared the University of Harderwijk.